This question has been discussed a few times on various grammar & language websites. At answers.yahoo.com the concensus is:

When expanded, these represent the same words: you are not. In that regard, there's no difference.
Keep in mind that neither expression should be used in formal writing because contractions are considered somewhat informal.

At wordreference.com one poster rants against "we aren't, they aren't, you aren't etc.; while another writes: "We're not going stresses the not.
We aren't going does not stress anything"; and a third argues by analogy with I'm not being preferred to I amn't or I ain't.

The longer thread of comments at reddit.com seems more useful than the two references already mentioned; it gives several examples are given where one form may be more natural than the other, such as:

a: I'm a computer programmer. b: No, you're not.

a: I'm going home now. b: No, you aren't.

The reddit thread includes examples of different emphases (much as before), and also digresses into inconclusive mention of You'rn't, You'ren't, and shouldn't've.

I disagree with the idea that there's some meaningful difference in emphasis between the two forms, and I don't think there are really any contexts where they're not interchangeable.

The main difference is simply that You're not is more common. I think that's just because we usually start by contracting at the first available point. We haven't consciously registered that there's another potential contraction point immediately following - we can only use one or the other, so usually we're already committed to the first one before the second comes along.